Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold166
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2719372
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17868 characters in sequence are not A, C, G, or T
File 7 of 18
Found at i:1094569 original size:17 final size:17
Alignment explanation
Indices: 1094516--1094569 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1094506 ATAAAATTTT
1094516 TATTTTAAATTTAATAA
1 TATTTTAAATTTAATAA
* *
1094533 TA-TTTAGAA-TGAATAT
1 TATTTTA-AATTTAATAA
*
1094549 TATTTTTAATTTAATAA
1 TATTTTAAATTTAATAA
1094566 TATT
1 TATT
1094570 AGAAAAGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TATTTTAAATTTAATAA
Found at i:1094636 original size:26 final size:26
Alignment explanation
Indices: 1094590--1094640 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
1094580 AATAAGATTT
*
1094590 AAAATTTTTTTAAAGATATAATTTTAA
1 AAAATTTTATTAAAGA-ATAATTTTAA
1094617 AAAATTATTATTAAAG-ATAATTTT
1 AAAATT-TTATTAAAGAATAATTTT
1094641 TTATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 6 0.27
28 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
AAAATTTTATTAAAGAATAATTTTAA
Found at i:1094650 original size:20 final size:20
Alignment explanation
Indices: 1094621--1094658 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1094611 TTTTAAAAAA
*
1094621 TTATTATTAAAGATAATTTT
1 TTATTATTAAAGACAATTTT
*
1094641 TTATTTTTAAAGACAATT
1 TTATTATTAAAGACAATT
1094659 AACCGTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
TTATTATTAAAGACAATTTT
Found at i:1097836 original size:27 final size:27
Alignment explanation
Indices: 1097785--1097864 Score: 67
Period size: 27 Copynumber: 2.9 Consensus size: 27
1097775 TCCTTTATTT
*
1097785 TTAAACATTTT-ATATAGAT-TATAAATAA
1 TTAAA-ATTTTAAT-TAGATAT-TAAAAAA
*
1097813 TTAAAATTTTATCTTA-ATATTAAAAAA
1 TTAAAATTTTA-ATTAGATATTAAAAAA
* *
1097840 TTTATATTTTAATTAGATATTAAAA
1 TTAAAATTTTAATTAGATATTAAAA
1097865 TAGAACTTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
26 3 0.07
27 31 0.72
28 8 0.19
29 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (27 bp):
TTAAAATTTTAATTAGATATTAAAAAA
Found at i:1102755 original size:13 final size:13
Alignment explanation
Indices: 1102739--1102763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1102729 CCCTTTTTGT
1102739 TTCAAAAATAATG
1 TTCAAAAATAATG
1102752 TTCAAAAATAAT
1 TTCAAAAATAAT
1102764 CTCCCCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (13 bp):
TTCAAAAATAATG
Found at i:1102825 original size:26 final size:26
Alignment explanation
Indices: 1102796--1102848 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1102786 TATTTCTCAA
1102796 AATATCTCTCCCCCTTTAACAAATTT
1 AATATCTCTCCCCCTTTAACAAATTT
* *
1102822 AATATCTCTCCCCTTTTTACAAATTT
1 AATATCTCTCCCCCTTTAACAAATTT
1102848 A
1 A
1102849 TTTTCAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.42
Consensus pattern (26 bp):
AATATCTCTCCCCCTTTAACAAATTT
Found at i:1111906 original size:25 final size:24
Alignment explanation
Indices: 1111878--1111931 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1111868 TTATTGTTGG
*
1111878 TTTTAAATGCTTTTATGAAAAATAT
1 TTTTAAAT-CTTTTATGAAAAATAA
* * *
1111903 TTTTATATTTTTTATGCAAAATAA
1 TTTTAAATCTTTTATGAAAAATAA
1111927 TTTTA
1 TTTTA
1111932 TTGAAAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (24 bp):
TTTTAAATCTTTTATGAAAAATAA
Found at i:1116385 original size:13 final size:13
Alignment explanation
Indices: 1116367--1116391 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1116357 ATAAGATTAA
1116367 TTCACTTTTAATG
1 TTCACTTTTAATG
1116380 TTCACTTTTAAT
1 TTCACTTTTAAT
1116392 CCTGAGCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (13 bp):
TTCACTTTTAATG
Found at i:1116867 original size:19 final size:20
Alignment explanation
Indices: 1116843--1116896 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
1116833 ACATTATGCT
*
1116843 TTGTATCGATACATGCT-TA
1 TTGTATCGATACATGCTCAA
*
1116862 TTGTATCGATACATACTCAA
1 TTGTATCGATACATGCTCAA
*
1116882 TTGTATCAATACATG
1 TTGTATCGATACATG
1116897 AAACTGGTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGCTCAA
Found at i:1117170 original size:29 final size:29
Alignment explanation
Indices: 1117128--1117184 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1117118 GTATGTCAAT
*
1117128 ATTCTAGCCTATAAATTTGAGTTGCCAAC
1 ATTCTAGCCTATAAAGTTGAGTTGCCAAC
1117157 ATTCTAGCCTATAAAGTTGAGTTGCCAA
1 ATTCTAGCCTATAAAGTTGAGTTGCCAA
1117185 TAGCTGAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (29 bp):
ATTCTAGCCTATAAAGTTGAGTTGCCAAC
Found at i:1125699 original size:14 final size:14
Alignment explanation
Indices: 1125682--1125712 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1125672 GATTTATAGG
1125682 TATTTATATCGATT
1 TATTTATATCGATT
*
1125696 TATTTATATCTATT
1 TATTTATATCGATT
1125710 TAT
1 TAT
1125713 ACACATCCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (14 bp):
TATTTATATCGATT
Found at i:1125762 original size:13 final size:13
Alignment explanation
Indices: 1125744--1125768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1125734 CATTATGCAT
1125744 TGTATCGATACAA
1 TGTATCGATACAA
1125757 TGTATCGATACA
1 TGTATCGATACA
1125769 TGCTTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1125787 original size:32 final size:33
Alignment explanation
Indices: 1125723--1125787 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
1125713 ACACATCCAG
* *
1125723 ATGTATCGATACATTATGCATTGTATCGATACA
1 ATGTATCGATACATGATGCATTGTATCAATACA
* * *
1125756 ATGTATCGATACATGCT-TATTGTATTAATACA
1 ATGTATCGATACATGATGCATTGTATCAATACA
1125788 TACTCAATTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (33 bp):
ATGTATCGATACATGATGCATTGTATCAATACA
Found at i:1125806 original size:20 final size:19
Alignment explanation
Indices: 1125757--1125808 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1125747 ATCGATACAA
* *
1125757 TGTATCGATACATGCTTAT
1 TGTATCGATACATACTAAT
**
1125776 TGTATTAATACATACTCAAT
1 TGTATCGATACATACT-AAT
1125796 TGTATCGATACAT
1 TGTATCGATACAT
1125809 GAAACTGGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATACTAAT
Found at i:1133085 original size:51 final size:52
Alignment explanation
Indices: 1133029--1133146 Score: 168
Period size: 51 Copynumber: 2.3 Consensus size: 52
1133019 TTTTCAAAAA
* * * *
1133029 GATACTCCAACCCCGTTTTTACTTCCAAAATATTTAATTT-TTCATCTC-GGG
1 GATACTCCAACCCCATTTTTACTT-CAAAACATTGAATTTCTTCATCTCTAGG
*
1133080 GATACTCCAACCCCATTTTTACTTCTAAACATTGAATTTCTTCATCTCTAGG
1 GATACTCCAACCCCATTTTTACTTCAAAACATTGAATTTCTTCATCTCTAGG
1133132 GATACTCCAACCCCA
1 GATACTCCAACCCCA
1133147 CCATTTTCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
50 12 0.20
51 31 0.52
52 17 0.28
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.36
Consensus pattern (52 bp):
GATACTCCAACCCCATTTTTACTTCAAAACATTGAATTTCTTCATCTCTAGG
Found at i:1133213 original size:79 final size:78
Alignment explanation
Indices: 1133079--1133416 Score: 297
Period size: 79 Copynumber: 4.3 Consensus size: 78
1133069 TTCATCTCGG
* * *
1133079 GGATACTCCAACCCCATTTTTACTTCT-AAACATTGAATTTCTTCATCTCTA-GGGATACTCCAA
1 GGATACTCCAACCCCA-TTTTACTTCTAAAACACTAAAATT-TTCATCTC-AGGGGATACTCCAA
*
1133142 CCCCACCAT-TTTCAAA
63 CCCCACCATCTCT-AAA
* *
1133158 GGCATACTCCAACCCCATTTTACTTCTAAAACACTAAAATTTTCATCTCAGGGGATACTCTAATC
1 GG-ATACTCCAACCCCATTTTACTTCTAAAACACTAAAATTTTCATCTCAGGGGATACTCCAACC
* * * * *
1133223 TCACTATTTTTGAGA
65 CCACCATCTCT-AAA
* * ** * * * * * *
1133238 GGATACTCTAA-CCCATTTTTATTTCCCAAACATTGAATTTTTTATCTCTGGGGATACTCTAACC
1 GGATACTCCAACCCCA-TTTTACTTCTAAAACACTAAAATTTTCATCTCAGGGGATACTCCAACC
* *
1133302 CTACCATCTCTAAGG
65 CCACCATCTCTAA-A
*** * * *
1133317 GGATACTCCAACCTTGTTTTACTTCTAAAACACCAAAATTTTCATCTCAAGGGATACTCCAACCT
1 GGATACTCCAACCCCATTTTACTTCTAAAACACTAAAATTTTCATCTCAGGGGATACTCCAACCC
1133382 CACCATCTCTAAGA
66 CACCATCTCTAA-A
1133396 GGATACTCCAACCCCGATTTT
1 GGATACTCCAACCCC-ATTTT
1133417 CACCAAAAAT
Statistics
Matches: 204, Mismatches: 47, Indels: 15
0.77 0.18 0.06
Matches are distributed among these distances:
78 6 0.03
79 162 0.79
80 36 0.18
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.33
Consensus pattern (78 bp):
GGATACTCCAACCCCATTTTACTTCTAAAACACTAAAATTTTCATCTCAGGGGATACTCCAACCC
CACCATCTCTAAA
Found at i:1133308 original size:158 final size:158
Alignment explanation
Indices: 1133079--1133409 Score: 432
Period size: 158 Copynumber: 2.1 Consensus size: 158
1133069 TTCATCTCGG
*
1133079 GGATACTCCAACCCCATTTTTACTTCTAAACATTGAATTTCTTCATCTCTAGGGATACTCCAACC
1 GGATACTCCAA-CCCATTTTTACTTCCAAACATTGAATTTCTTCATCTCTAGGGATACTCCAACC
* *
1133144 CCACCAT-TTTCAAAGGCATACTCCAACCCCATTTTACTTCTAAAACACTAAAATTTTCATCTCA
65 CCACCATCTCT-AAAGGCATACTCCAACCCCATTTTACTTCTAAAACACCAAAATTTTCATCTCA
* * * * * * *
1133208 GGGGATACTCTAATCTCACTATTTTTGAGA
129 AGGGATACTCCAACCTCACCATCTCTAAGA
* * * * *
1133238 GGATACTCTAACCCATTTTTATTTCCCAAACATTGAATTT-TTTATCTCTGGGGATACTCTAACC
1 GGATACTCCAACCCATTTTTACTT-CCAAACATTGAATTTCTTCATCTCTAGGGATACTCCAACC
* * * ***
1133302 CTACCATCTCTAAGGGGATACTCCAACCTTGTTTTACTTCTAAAACACCAAAATTTTCATCTCAA
65 CCACCATCTCTAAAGGCATACTCCAACCCCATTTTACTTCTAAAACACCAAAATTTTCATCTCAA
1133367 GGGATACTCCAACCTCACCATCTCTAAGA
130 GGGATACTCCAACCTCACCATCTCTAAGA
1133396 GGATACTCCAACCC
1 GGATACTCCAACCC
1133410 CGATTTTCAC
Statistics
Matches: 148, Mismatches: 22, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
158 122 0.82
159 26 0.18
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (158 bp):
GGATACTCCAACCCATTTTTACTTCCAAACATTGAATTTCTTCATCTCTAGGGATACTCCAACCC
CACCATCTCTAAAGGCATACTCCAACCCCATTTTACTTCTAAAACACCAAAATTTTCATCTCAAG
GGATACTCCAACCTCACCATCTCTAAGA
Found at i:1141890 original size:28 final size:28
Alignment explanation
Indices: 1141822--1141903 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 28
1141812 ATTGAAAAAT
* *
1141822 AAGAAAGATC-AAGGAAGTGAAATCAAC
1 AAGAAATATCAAAGGAAATGAAATCAAC
*
1141849 AAGAAATATGAAAGGAAATGAAAT-AAGC
1 AAGAAATATCAAAGGAAATGAAATCAA-C
*
1141877 AAGAAACT-TCAAAGGAAAAGAAATCAA
1 AAGAAA-TATCAAAGGAAATGAAATCAA
1141904 TAAAGAAGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
27 10 0.22
28 33 0.72
29 3 0.07
ACGTcount: A:0.60, C:0.09, G:0.20, T:0.12
Consensus pattern (28 bp):
AAGAAATATCAAAGGAAATGAAATCAAC
Found at i:1141975 original size:10 final size:9
Alignment explanation
Indices: 1141958--1141989 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1141948 CTAATAACTA
1141958 TCTTTTTTT
1 TCTTTTTTT
1141967 TCTTTTTTT
1 TCTTTTTTT
1141976 TC-TTTTTT
1 TCTTTTTTT
1141984 TCTTTT
1 TCTTTT
1141990 GATGACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:1142665 original size:29 final size:29
Alignment explanation
Indices: 1142618--1142726 Score: 96
Period size: 29 Copynumber: 3.8 Consensus size: 29
1142608 AACAATAGGC
* **
1142618 CCATAAATACATGTGAATTGGGCTCCAAG
1 CCATGAATACATGCAAATTGGGCTCCAAG
* **
1142647 CCATGAATACATGCAAATTGGGCTTCACT
1 CCATGAATACATGCAAATTGGGCTCCAAG
* * **
1142676 CTTCTTG--GACATGTGAATTGGGCTCCAAG
1 C--CATGAATACATGCAAATTGGGCTCCAAG
1142705 CCATGAATACATGCAAATTGGG
1 CCATGAATACATGCAAATTGGG
1142727 TTTCACTCTT
Statistics
Matches: 59, Mismatches: 17, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
27 3 0.05
29 53 0.90
31 3 0.05
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (29 bp):
CCATGAATACATGCAAATTGGGCTCCAAG
Found at i:1142716 original size:58 final size:58
Alignment explanation
Indices: 1142626--1142763 Score: 240
Period size: 58 Copynumber: 2.4 Consensus size: 58
1142616 GCCCATAAAT
*
1142626 ACATGTGAATTGGGCTCCAAGCCATGAATACATGCAAATTGGGCTTCACTCTTCTTGG
1 ACATGTGAATTGGGCTCCAAGCCATGAATACATGCAAATTGGGCTTCACTCTTCTTGC
*
1142684 ACATGTGAATTGGGCTCCAAGCCATGAATACATGCAAATTGGGTTTCACTCTTCTTGC
1 ACATGTGAATTGGGCTCCAAGCCATGAATACATGCAAATTGGGCTTCACTCTTCTTGC
**
1142742 ACATACGAATTGGGCTCCAAGC
1 ACATGTGAATTGGGCTCCAAGC
1142764 TTTATTCTTC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 76 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (58 bp):
ACATGTGAATTGGGCTCCAAGCCATGAATACATGCAAATTGGGCTTCACTCTTCTTGC
Found at i:1160739 original size:24 final size:24
Alignment explanation
Indices: 1160716--1160795 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
1160706 TTATCTCTCT
*
1160716 TATCTCTCCTCCTATCATCCCTCT
1 TATCTCTCCTCCTATCATCCCTCC
* * * *
1160740 TATCTCTCCTGTCTCTCCTGTCTCTCC
1 TATCTCTCCT-CCTAT-C-ATCCCTCC
*
1160767 TATCTCTCCTCTTATCATCCCTCC
1 TATCTCTCCTCCTATCATCCCTCC
1160791 TATCT
1 TATCT
1160796 TTTTTTTCTT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
24 21 0.49
25 4 0.09
26 3 0.07
27 15 0.35
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (24 bp):
TATCTCTCCTCCTATCATCCCTCC
Found at i:1160755 original size:51 final size:51
Alignment explanation
Indices: 1160694--1160795 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
1160684 CTTGTCATCC
* * *
1160694 CTCCTCTCTCTATTATCTCTCTTATCTCTCCTCCTATCATCCCTCTTATCT
1 CTCCTCTCTCTACTATCTCTCCTATCTCTCCTCCTATCATCCCTCCTATCT
* * * *
1160745 CTCCTGTCTCTCCTGTCTCTCCTATCTCTCCTCTTATCATCCCTCCTATCT
1 CTCCTCTCTCTACTATCTCTCCTATCTCTCCTCCTATCATCCCTCCTATCT
1160796 TTTTTTTCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.10, C:0.43, G:0.02, T:0.45
Consensus pattern (51 bp):
CTCCTCTCTCTACTATCTCTCCTATCTCTCCTCCTATCATCCCTCCTATCT
Found at i:1160775 original size:9 final size:9
Alignment explanation
Indices: 1160740--1160776 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1160730 TCATCCCTCT
1160740 TATCTCTCC
1 TATCTCTCC
*
1160749 TGTCTCTCC
1 TATCTCTCC
*
1160758 TGTCTCTCC
1 TATCTCTCC
1160767 TATCTCTCC
1 TATCTCTCC
1160776 T
1 T
1160777 CTTATCATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.05, C:0.43, G:0.05, T:0.46
Consensus pattern (9 bp):
TATCTCTCC
Found at i:1170838 original size:12 final size:11
Alignment explanation
Indices: 1170816--1170891 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1170806 AGAGAAAGAA
*
1170816 GAGAGAGGAGG
1 GAGATAGGAGG
1170827 GATGATAGGAGG
1 GA-GATAGGAGG
*
1170839 AGAGACAGGA--
1 -GAGATAGGAGG
*
1170849 GAGATAGTA--
1 GAGATAGGAGG
1170858 GAGATAGGAGG
1 GAGATAGGAGG
1170869 GATGATAGGAGG
1 GA-GATAGGAGG
*
1170881 AGAGACAGGAG
1 -GAGATAGGAG
1170892 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1170848 original size:24 final size:24
Alignment explanation
Indices: 1170815--1170900 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1170805 AAGAGAAAGA
*
1170815 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1170839 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1170857 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1170881 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1170901 AGAGAGGAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1170850 original size:9 final size:9
Alignment explanation
Indices: 1170836--1170913 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
1170826 GGATGATAGG
*
1170836 AGGAGAGAC
1 AGGAGAGAT
1170845 AGGAGAGAT
1 AGGAGAGAT
*
1170854 AGTAGAGAT
1 AGGAGAGAT
*
1170863 AGGAGGGAT
1 AGGAGAGAT
* *
1170872 --GATAG-G
1 AGGAGAGAT
*
1170878 AGGAGAGAC
1 AGGAGAGAT
1170887 AGGAGAGAT
1 AGGAGAGAT
** *
1170896 AATAGAGAG
1 AGGAGAGAT
1170905 AGGAGAGAT
1 AGGAGAGAT
1170914 GACAGGAGGA
Statistics
Matches: 50, Mismatches: 16, Indels: 6
0.69 0.22 0.08
Matches are distributed among these distances:
7 3 0.06
8 4 0.08
9 43 0.86
ACGTcount: A:0.44, C:0.03, G:0.44, T:0.10
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:1170866 original size:18 final size:18
Alignment explanation
Indices: 1170839--1170913 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 18
1170829 TGATAGGAGG
1170839 AGAGACAGGAGAGATAGT
1 AGAGACAGGAGAGATAGT
* *
1170857 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGA--GA-GAT---AGT
*
1170881 AGAGACAGGAGAGATAAT
1 AGAGACAGGAGAGATAGT
*
1170899 AGAGAGAGGAGAGAT
1 AGAGACAGGAGAGAT
1170914 GACAGGAGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
18 24 0.53
20 2 0.04
21 6 0.13
22 2 0.04
24 11 0.24
ACGTcount: A:0.44, C:0.03, G:0.43, T:0.11
Consensus pattern (18 bp):
AGAGACAGGAGAGATAGT
Found at i:1170867 original size:42 final size:42
Alignment explanation
Indices: 1170806--1170924 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1170796 GTAGCCCTCA
* *
1170806 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1170848 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* * *
1170890 AGAGATAATAGAGAGAGGAGAGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1170925 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.44, C:0.03, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1177073 original size:64 final size:64
Alignment explanation
Indices: 1176972--1177098 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
1176962 TTTAGAACTC
*
1176972 CTGATGAGAACCAAGGAAGGTCCATTGAAGACAAAGACCTGAAGGCGTTGAAAAGG-TTTCAAGA
1 CTGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCTGAAGGCGTTG-AAAGGATTTCAAGA
*
1177036 CTGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCTGAAGGCGTTGGAAGGATTTCAAG
1 CTGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCTGAAGGCGTTGAAAGGATTTCAAG
1177099 GACCAATAAC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
63 4 0.07
64 56 0.93
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.17
Consensus pattern (64 bp):
CTGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCTGAAGGCGTTGAAAGGATTTCAAGA
Found at i:1178686 original size:12 final size:11
Alignment explanation
Indices: 1178664--1178739 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1178654 AGAGAAAGAA
*
1178664 GAGAGAGGAGG
1 GAGATAGGAGG
1178675 GATGATAGGAGG
1 GA-GATAGGAGG
*
1178687 AGAGACAGGA--
1 -GAGATAGGAGG
*
1178697 GAGATAGTA--
1 GAGATAGGAGG
1178706 GAGATAGGAGG
1 GAGATAGGAGG
1178717 GATGATAGGAGG
1 GA-GATAGGAGG
*
1178729 AGAGACAGGAG
1 -GAGATAGGAG
1178740 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1178696 original size:24 final size:24
Alignment explanation
Indices: 1178663--1178748 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1178653 AAGAGAAAGA
*
1178663 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1178687 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1178705 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1178729 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1178749 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1178715 original size:42 final size:42
Alignment explanation
Indices: 1178654--1178772 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1178644 TAGCCCTCAA
* *
1178654 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1178696 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1178738 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1178773 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1185889 original size:12 final size:11
Alignment explanation
Indices: 1185867--1185942 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1185857 AGAGAAAGAA
*
1185867 GAGACAGGAGG
1 GAGATAGGAGG
1185878 GATGATAGGAGG
1 GA-GATAGGAGG
*
1185890 AGAGACAGGA--
1 -GAGATAGGAGG
*
1185900 GAGATAGTA--
1 GAGATAGGAGG
1185909 GAGATAGGAGG
1 GAGATAGGAGG
1185920 GATGATAGGAGG
1 GA-GATAGGAGG
*
1185932 AGAGACAGGAG
1 -GAGATAGGAG
1185943 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.04, G:0.47, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1185897 original size:24 final size:24
Alignment explanation
Indices: 1185866--1185951 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
1185856 AAGAGAAAGA
1185866 AGAGACAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1185890 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1185908 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1185932 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1185952 AGAGAGGAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 29 0.58
ACGTcount: A:0.42, C:0.03, G:0.44, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1185918 original size:42 final size:42
Alignment explanation
Indices: 1185857--1185975 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1185847 TAGCCCTCAA
* *
1185857 AGAGAAAGAAGAGACAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGACAGGAGGGATGATAGGAGGAGAGACAGG
*
1185899 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGACAGGAGGGATGATAGGAGGAGAGACAGG
* * *
1185941 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGACAGGAGGGATGATAGGAGGAG
1185976 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGACAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1191013 original size:148 final size:146
Alignment explanation
Indices: 1190731--1191021 Score: 449
Period size: 148 Copynumber: 2.0 Consensus size: 146
1190721 TGATTGTGGC
* * *
1190731 GCCATCTTTCATCTCTAATCTATTCCATTTTGTTATTTTTTTTTGCTTCTTTCAAATTCTGTTCT
1 GCCATCCTCCATCTCTAATCTATTCCATTTTGTTATTTTTTCTTGCTTCTTTCAAATTCTGTTCT
* *
1190796 TGCATCAATATTCTGTTTATTGTTAGAAATCCATCTCAAGATCATTATTTAGGCAACCTTGGTTC
66 TGCATCAATATTCTGTTTATTGTTAGAAATCCAGCTCAAGATCATTATTTAGGCAACCTTGGATC
1190861 ATGGTTGTCATCAGGT
131 ATGGTTGTCATCAGGT
* *
1190877 GCCATCCTCCATCTCTATTCTATTCCAGTTTTGTTATTTTTTCTT-CTTCTTTCAATTTCTGTTC
1 GCCATCCTCCATCTCTAATCTATTCCA-TTTTGTTATTTTTTCTTGCTTCTTTCAAATTCTGTTC
* * * *
1190941 TTGCATTAATAATTCTATTTTGTTGTTAGAAATCCAGCTCAAGATCGTTATTTAGGCAACCTTGG
65 TTGCATCAAT-ATTCT-GTTTATTGTTAGAAATCCAGCTCAAGATCATTATTTAGGCAACCTTGG
1191006 ATCATGGTTGTCATCA
128 ATCATGGTTGTCATCA
1191022 ATTGGTATTA
Statistics
Matches: 131, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
146 51 0.39
147 21 0.16
148 59 0.45
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.47
Consensus pattern (146 bp):
GCCATCCTCCATCTCTAATCTATTCCATTTTGTTATTTTTTCTTGCTTCTTTCAAATTCTGTTCT
TGCATCAATATTCTGTTTATTGTTAGAAATCCAGCTCAAGATCATTATTTAGGCAACCTTGGATC
ATGGTTGTCATCAGGT
Found at i:1191937 original size:12 final size:11
Alignment explanation
Indices: 1191918--1191993 Score: 61
Period size: 12 Copynumber: 6.9 Consensus size: 11
1191908 AAAGAAAGAA
1191918 GAGATAGGAGG
1 GAGATAGGAGG
*
1191929 GATGATAGGTGG
1 GA-GATAGGAGG
1191941 AGAGATAGGA--
1 -GAGATAGGAGG
*
1191951 GAGATAGTA--
1 GAGATAGGAGG
1191960 GAGATAGGAGG
1 GAGATAGGAGG
*
1191971 GATGATAGCAGG
1 GA-GATAGGAGG
1191983 AGAGATAGGAG
1 -GAGATAGGAG
1191994 AGATAATGAG
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 16 0.30
11 4 0.08
12 29 0.55
13 4 0.08
ACGTcount: A:0.38, C:0.01, G:0.46, T:0.14
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1191948 original size:24 final size:24
Alignment explanation
Indices: 1191917--1191993 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 24
1191907 AAAAGAAAGA
1191917 AGAGATAGGAGGGATGATAGGTGG
1 AGAGATAGGAGGGATGATAGGTGG
1191941 AGAGATAGGA--GA-GATA-GT--
1 AGAGATAGGAGGGATGATAGGTGG
**
1191959 AGAGATAGGAGGGATGATAGCAGG
1 AGAGATAGGAGGGATGATAGGTGG
1191983 AGAGATAGGAG
1 AGAGATAGGAG
1191994 AGATAATGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
18 10 0.22
20 4 0.09
21 8 0.18
22 2 0.04
24 21 0.47
ACGTcount: A:0.39, C:0.01, G:0.45, T:0.14
Consensus pattern (24 bp):
AGAGATAGGAGGGATGATAGGTGG
Found at i:1191953 original size:9 final size:9
Alignment explanation
Indices: 1191939--1191998 Score: 63
Period size: 9 Copynumber: 7.0 Consensus size: 9
1191929 GATGATAGGT
1191939 GGAGAGATA
1 GGAGAGATA
1191948 GGAGAGATA
1 GGAGAGATA
*
1191957 GTAGAGATA
1 GGAGAGATA
*
1191966 GGAGGGAT-
1 GGAGAGATA
* *
1191974 -GATAG-CA
1 GGAGAGATA
1191981 GGAGAGATA
1 GGAGAGATA
1191990 GGAGAGATA
1 GGAGAGATA
1191999 ATGAGAGAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 33 0.82
ACGTcount: A:0.42, C:0.02, G:0.43, T:0.13
Consensus pattern (9 bp):
GGAGAGATA
Found at i:1191976 original size:42 final size:42
Alignment explanation
Indices: 1191917--1192016 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
1191907 AAAAGAAAGA
** *
1191917 AGAGATAGGAGGGATGATAGGTGGAGAGATAGGAGAGATAGT
1 AGAGATAGGAGGGATGATAGCAGGAGAGATAGGAGAGATAAT
1191959 AGAGATAGGAGGGATGATAGCAGGAGAGATAGGAGAGATAAT
1 AGAGATAGGAGGGATGATAGCAGGAGAGATAGGAGAGATAAT
*
1192001 -GAGAGAGGAGGGATGA
1 AGAGATAGGAGGGATGA
1192017 AAAGAGGAGG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
41 15 0.28
42 39 0.72
ACGTcount: A:0.40, C:0.01, G:0.45, T:0.14
Consensus pattern (42 bp):
AGAGATAGGAGGGATGATAGCAGGAGAGATAGGAGAGATAAT
Found at i:1194915 original size:18 final size:18
Alignment explanation
Indices: 1194892--1194932 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1194882 TGATAGGAGG
*
1194892 AGAGATAGCAGAGATAGT
1 AGAGATAGCAGAGATAAT
* *
1194910 AGAGATAGGATAGATAAT
1 AGAGATAGCAGAGATAAT
1194928 AGAGA
1 AGAGA
1194933 GAGGAGGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.32, T:0.17
Consensus pattern (18 bp):
AGAGATAGCAGAGATAAT
Found at i:1194937 original size:18 final size:18
Alignment explanation
Indices: 1194903--1194937 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1194893 GAGATAGCAG
* *
1194903 AGATAGTAGAGATAGGAT
1 AGATAATAGAGAGAGGAT
1194921 AGATAATAGAGAGAGGA
1 AGATAATAGAGAGAGGA
1194938 GGGATGACAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.34, T:0.17
Consensus pattern (18 bp):
AGATAATAGAGAGAGGAT
Found at i:1198016 original size:11 final size:11
Alignment explanation
Indices: 1198002--1198038 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1197992 AGGATAATAT
1198002 AATAAGTATAA
1 AATAAGTATAA
1198013 AATAAGTAT-A
1 AATAAGTATAA
1198023 AATAAGTATAA
1 AATAAGTATAA
*
1198034 TATAA
1 AATAA
1198039 TAAGGAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (11 bp):
AATAAGTATAA
Found at i:1198026 original size:21 final size:19
Alignment explanation
Indices: 1197974--1198040 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
1197964 AGATTTACTT
* *
1197974 ATAATAGAATAAGTAATAAGG
1 ATAATATAATAAGT-ATAA-A
1197995 ATAATATAATAAGTATAAA
1 ATAATATAATAAGTATAAA
*
1198014 ATAAGTATAAATAAGTATAAT
1 ATAA-TAT-AATAAGTATAAA
1198035 ATAATA
1 ATAATA
1198041 AGGAATGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.10
20 9 0.22
21 28 0.68
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (19 bp):
ATAATATAATAAGTATAAA
Found at i:1201279 original size:24 final size:22
Alignment explanation
Indices: 1201245--1201293 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
1201235 TGTCATCCCT
* *
1201245 TCTCTCTCTATTATCTCTCCTA
1 TCTCTCTCTATCATCCCTCCTA
1201267 TCTCTCCTCCTATCATCCCTCCTA
1 TCTCT-CT-CTATCATCCCTCCTA
1201291 TCT
1 TCT
1201294 GTACTATCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 2 0.09
24 16 0.70
ACGTcount: A:0.12, C:0.43, G:0.00, T:0.45
Consensus pattern (22 bp):
TCTCTCTCTATCATCCCTCCTA
Found at i:1201347 original size:42 final size:42
Alignment explanation
Indices: 1201208--1201347 Score: 149
Period size: 42 Copynumber: 3.3 Consensus size: 42
1201198 TTTTCTCTCA
* * * *
1201208 CTCTTCCATCTTCTTCTCTC-CTCCTCCTGTCATCCCTTCTCT
1 CTCTTCTATC-TCTTCTATCTCTCCTCCTGTCATCCCTCCTAT
* *
1201250 CTCTAT-TATCTCTCCTATCTCTCCTCCTATCATCCCTCCTAT
1 CTCT-TCTATCTCTTCTATCTCTCCTCCTGTCATCCCTCCTAT
* * * *
1201292 CTGTACTATCTCTTCTATCTCTCCTCATGTCATTCCTCCTAT
1 CTCTTCTATCTCTTCTATCTCTCCTCCTGTCATCCCTCCTAT
*
1201334 CTCTTCTTTCTCTT
1 CTCTTCTATCTCTT
1201348 TAAGGGCTAC
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 7 0.09
42 72 0.90
43 1 0.01
ACGTcount: A:0.10, C:0.41, G:0.02, T:0.46
Consensus pattern (42 bp):
CTCTTCTATCTCTTCTATCTCTCCTCCTGTCATCCCTCCTAT
Found at i:1215193 original size:42 final size:42
Alignment explanation
Indices: 1215138--1215256 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1215128 TTCTTCTCTC
* *
1215138 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
1215180 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1215222 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1215257 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1215197 original size:12 final size:11
Alignment explanation
Indices: 1215171--1215246 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1215161 TCTATTATCT
*
1215171 CTCCTGTCTCTC
1 CTCCTATCTC-C
1215183 CTCCTATCATCC
1 CTCCTATC-TCC
1215195 CTCCTATCT--
1 CTCCTATCTCC
*
1215204 CTACTATCT--
1 CTCCTATCTCC
*
1215213 CTCCTGTCTCTC
1 CTCCTATCTC-C
1215225 CTCCTATCATCC
1 CTCCTATC-TCC
*
1215237 CTCCTCTCTC
1 CTCCTATCTC
1215247 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:1215198 original size:24 final size:24
Alignment explanation
Indices: 1215162--1215247 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1215152 CCTCCTCTCT
* *
1215162 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1215186 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1215207 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1215228 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1215248 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1215222 original size:18 final size:18
Alignment explanation
Indices: 1215153--1215223 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1215143 CCTGTCATCC
* *
1215153 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
1215171 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
1215193 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
1215213 CTCCTGTCTCT
1 CTCCTGTCTCT
1215224 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:1218450 original size:12 final size:11
Alignment explanation
Indices: 1218428--1218482 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
1218418 AGAGAAAGAA
*
1218428 GAGATAAGAGG
1 GAGATAGGAGG
1218439 GATGATAGGAGG
1 GA-GATAGGAGG
*
1218451 AGAGATAGTA--
1 -GAGATAGGAGG
1218461 GAGATAGGAGG
1 GAGATAGGAGG
1218472 GATGATAGGAG
1 GA-GATAGGAG
1218483 AAGAGATATG
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
9 8 0.22
11 4 0.11
12 22 0.61
13 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.45, T:0.15
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1218489 original size:33 final size:33
Alignment explanation
Indices: 1218417--1218500 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
1218407 GTAGCCCTTA
* *
1218417 AAGAGAAAGAAGAGATAAGAGGGATGATAGGAG
1 AAGAGATAGTAGAGATAAGAGGGATGATAGGAG
* *
1218450 GAGAGATAGTAGAGATAGGAGGGATGATAGGAG
1 AAGAGATAGTAGAGATAAGAGGGATGATAGGAG
1218483 AAGAGATA-TGAGAGATAA
1 AAGAGATAGT-AGAGATAA
1218501 TAGAGAGAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
32 1 0.02
33 43 0.98
ACGTcount: A:0.48, C:0.00, G:0.39, T:0.13
Consensus pattern (33 bp):
AAGAGATAGTAGAGATAAGAGGGATGATAGGAG
Found at i:1218503 original size:24 final size:25
Alignment explanation
Indices: 1218460--1218508 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1218450 GAGAGATAGT
* *
1218460 AGAGATAGGAGGGATGATAG-GAGA
1 AGAGATAGGAGAGATAATAGAGAGA
*
1218484 AGAGATATGAGAGATAATAGAGAGA
1 AGAGATAGGAGAGATAATAGAGAGA
1218509 GGAGGGATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.39, T:0.14
Consensus pattern (25 bp):
AGAGATAGGAGAGATAATAGAGAGA
Found at i:1220636 original size:12 final size:11
Alignment explanation
Indices: 1220617--1220692 Score: 61
Period size: 12 Copynumber: 6.9 Consensus size: 11
1220607 AAAGAAAGAA
1220617 GAGATAGGAGG
1 GAGATAGGAGG
1220628 GATGATAGGAGG
1 GA-GATAGGAGG
*
1220640 AGAAATAGGA--
1 -GAGATAGGAGG
*
1220650 GAGATAGTA--
1 GAGATAGGAGG
1220659 GAGATAGGAGG
1 GAGATAGGAGG
*
1220670 GATGATAGGAGAA
1 GA-GATAGGAG-G
1220683 GAGATAGGAG
1 GAGATAGGAG
1220693 AGATAATAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.07
12 31 0.57
13 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.13
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1220651 original size:9 final size:9
Alignment explanation
Indices: 1220637--1220697 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 9
1220627 GGATGATAGG
*
1220637 AGGAGAAAT
1 AGGAGAGAT
1220646 AGGAGAGAT
1 AGGAGAGAT
*
1220655 AGTAGAGAT
1 AGGAGAGAT
1220664 AGGAGGGATGAT
1 AGGA--GA-GAT
1220676 AGGAGAAGAGAT
1 A-G-G-AGAGAT
1220688 AGGAGAGAT
1 AGGAGAGAT
1220697 A
1 A
1220698 ATAGAGAGAG
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
9 26 0.60
10 1 0.02
11 3 0.07
12 8 0.19
13 3 0.07
14 1 0.02
15 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.41, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:1220675 original size:42 final size:42
Alignment explanation
Indices: 1220616--1220725 Score: 175
Period size: 42 Copynumber: 2.6 Consensus size: 42
1220606 AAAAGAAAGA
* *
1220616 AGAGATAGGAGGGATGATAGGAGGAGAAATAGGAGAGATAGT
1 AGAGATAGGAGGGATGATAGGAGAAGAAATAGGAGAGATAAT
*
1220658 AGAGATAGGAGGGATGATAGGAGAAGAGATAGGAGAGATAAT
1 AGAGATAGGAGGGATGATAGGAGAAGAAATAGGAGAGATAAT
* *
1220700 AGAGAGAGGAGGGATGACAGGAGAAG
1 AGAGATAGGAGGGATGATAGGAGAAG
1220726 GAGAGAAGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.44, C:0.01, G:0.44, T:0.12
Consensus pattern (42 bp):
AGAGATAGGAGGGATGATAGGAGAAGAAATAGGAGAGATAAT
Found at i:1220701 original size:12 final size:12
Alignment explanation
Indices: 1220661--1220706 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1220651 AGATAGTAGA
*
1220661 GATAGGAGGGAT
1 GATAGGAGAGAT
1220673 GATAGGAGAAGA-
1 GATAGGAG-AGAT
1220685 GATAGGAGAGAT
1 GATAGGAGAGAT
*
1220697 AATA-GAGAGA
1 GATAGGAGAGA
1220707 GGAGGGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 9 0.30
12 19 0.63
13 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.41, T:0.13
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:1227876 original size:42 final size:42
Alignment explanation
Indices: 1227821--1227939 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1227811 TTCTTCTCTC
* *
1227821 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1227863 CTCCTCCTATCATCCCTCCTATCTTTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1227905 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1227940 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1227881 original size:24 final size:24
Alignment explanation
Indices: 1227845--1227930 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1227835 CCTCCTCTCT
* *
1227845 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1227869 CTATCATCCCTCCTATCT-T--TA
1 CTATCATCCCTCCTGTCTCTCCTC
1227890 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1227911 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1227931 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 8 0.16
19 1 0.02
20 1 0.02
21 12 0.24
22 1 0.02
23 1 0.02
24 25 0.51
ACGTcount: A:0.10, C:0.44, G:0.02, T:0.43
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1229164 original size:243 final size:242
Alignment explanation
Indices: 1228873--1229357 Score: 943
Period size: 243 Copynumber: 2.0 Consensus size: 242
1228863 GACAACCATG
*
1228873 AACCAAGGTTGCCTAAATAATGATCTTGAGATGGATTTCTAACAATAAACAGAATTATTGATGCA
1 AACCAAGGTTGCATAAATAATGATCTTGAGATGGATTTCTAACAATAAACAGAATTATTGATGCA
1228938 AAAAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATGGAATAGATTAGAGATGAAGGATG
66 AAAAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATGGAATAGATTAGAGATGAAGGATG
1229003 GCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTCTTGGCCTCTTGAT
131 GCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTCTTGGCCTCTTGAT
1229068 AAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAGAATCACTCTCA
196 AAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAGAATCACTCTCA
*
1229115 AACCAAGGTTGTCATCAATAATGATCTTGAGATGGATTTCTAACAATAAACAGAATTATTGATGC
1 AACCAAGGTTG-CATAAATAATGATCTTGAGATGGATTTCTAACAATAAACAGAATTATTGATGC
1229180 AAAAAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATGGAATAGATTAGAGATGAAGGAT
65 AAAAAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATGGAATAGATTAGAGATGAAGGAT
1229245 GGCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTCTTGGCCTCTTGA
130 GGCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTCTTGGCCTCTTGA
1229310 TAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAGAATCACTCTCA
195 TAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAGAATCACTCTCA
1229358 CACAAAAATG
Statistics
Matches: 240, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
242 11 0.05
243 229 0.95
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (242 bp):
AACCAAGGTTGCATAAATAATGATCTTGAGATGGATTTCTAACAATAAACAGAATTATTGATGCA
AAAAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATGGAATAGATTAGAGATGAAGGATG
GCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTCTTGGCCTCTTGAT
AAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAGAATCACTCTCA
Found at i:1232817 original size:15 final size:15
Alignment explanation
Indices: 1232799--1232852 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
1232789 CTTCTTCTCT
*
1232799 CCTCCTCCTGTCATC
1 CCTCCTCCTATCATC
*
1232814 CCTCCTCTCTCTATTATC
1 CCT-C-CTC-CTATCATC
*
1232832 TCTCCTCCTATCATC
1 CCTCCTCCTATCATC
1232847 CCTCCT
1 CCTCCT
1232853 ATCTCTACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 15 0.48
16 4 0.13
17 4 0.13
18 8 0.26
ACGTcount: A:0.09, C:0.50, G:0.02, T:0.39
Consensus pattern (15 bp):
CCTCCTCCTATCATC
Found at i:1232836 original size:18 final size:18
Alignment explanation
Indices: 1232815--1232876 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
1232805 CCTGTCATCC
1232815 CTCCTCTCTCTATTATCT
1 CTCCTCTCTCTATTATCT
* *
1232833 CT-C-CTC-CTATCATCC
1 CTCCTCTCTCTATTATCT
* *
1232848 CTCCTATCTCTACTATCT
1 CTCCTCTCTCTATTATCT
*
1232866 CTCCTGTCTCT
1 CTCCTCTCTCT
1232877 CCTCCTATCA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 9 0.26
16 4 0.12
17 3 0.09
18 18 0.53
ACGTcount: A:0.11, C:0.44, G:0.02, T:0.44
Consensus pattern (18 bp):
CTCCTCTCTCTATTATCT
Found at i:1232846 original size:33 final size:33
Alignment explanation
Indices: 1232800--1232870 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1232790 TTCTTCTCTC
* * *
1232800 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCT
1232833 CTCCTCCTATCATCCCTCCTATCTCTACTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCT
1232866 CTCCT
1 CTCCT
1232871 GTCTCTCCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.46, G:0.01, T:0.41
Consensus pattern (33 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCT
Found at i:1232850 original size:12 final size:11
Alignment explanation
Indices: 1232828--1232899 Score: 53
Period size: 12 Copynumber: 6.5 Consensus size: 11
1232818 CTCTCTCTAT
1232828 TATCTCTCCTCC
1 TATCTC-CCTCC
1232840 TATCATCCCTCC
1 TATC-TCCCTCC
*
1232852 TATCT--CTAC
1 TATCTCCCTCC
1232861 TATCT--CTCC
1 TATCTCCCTCC
*
1232870 TGTCTCTCCTCC
1 TATCTC-CCTCC
1232882 TATCATCCCTCC
1 TATC-TCCCTCC
*
1232894 TCTCTC
1 TATCTC
1232900 TTCTTTCTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
9 15 0.30
11 3 0.06
12 28 0.56
13 4 0.08
ACGTcount: A:0.11, C:0.47, G:0.01, T:0.40
Consensus pattern (11 bp):
TATCTCCCTCC
Found at i:1232876 original size:42 final size:42
Alignment explanation
Indices: 1232830--1232909 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
1232820 CTCTCTATTA
1232830 TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTG
1 TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTG
* * *
1232872 TCTCTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
1232910 TTGAGGGCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.09, C:0.46, G:0.01, T:0.44
Consensus pattern (42 bp):
TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTG
Found at i:1236191 original size:12 final size:12
Alignment explanation
Indices: 1236174--1236208 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1236164 TCTACTATCT
1236174 CTCCTATCTCTC
1 CTCCTATCTCTC
1236186 CTCCTATCATC-C
1 CTCCTATC-TCTC
1236198 CTCCTATCTCT
1 CTCCTATCTCT
1236209 TCTTTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.11, C:0.49, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:1239884 original size:12 final size:11
Alignment explanation
Indices: 1239862--1239933 Score: 53
Period size: 12 Copynumber: 6.5 Consensus size: 11
1239852 AGAGAAAGAA
*
1239862 GAGAGAGGAGG
1 GAGATAGGAGG
1239873 GATGATAGGAGG
1 GA-GATAGGAGG
*
1239885 AGAGACAGGA--
1 -GAGATAGGAGG
*
1239895 GAGATAGTA--
1 GAGATAGGAGG
1239904 GAGATAGGAGG
1 GAGATAGGAGG
1239915 GATGATAGGAGG
1 GA-GATAGGAGG
1239927 AGAGATA
1 -GAGATA
1239934 ATAGAGAGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
9 15 0.30
11 4 0.08
12 27 0.54
13 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.47, T:0.11
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1239913 original size:42 final size:42
Alignment explanation
Indices: 1239852--1239931 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
1239842 TAGCCCTCAA
1239852 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* * *
1239894 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGA
1 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGA
1239932 TAATAGAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.44, C:0.01, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1239928 original size:33 final size:33
Alignment explanation
Indices: 1239891--1239961 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1239881 GAGGAGAGAC
* * *
1239891 AGGAGAGATAGTAGAGATAGGAGGGATGATAGG
1 AGGAGAGATAATAGAGAGAGGAGGGATGACAGG
1239924 AGGAGAGATAATAGAGAGAGGAGGGATGACAGG
1 AGGAGAGATAATAGAGAGAGGAGGGATGACAGG
1239957 AGGAG
1 AGGAG
1239962 GAGAGAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.01, G:0.46, T:0.11
Consensus pattern (33 bp):
AGGAGAGATAATAGAGAGAGGAGGGATGACAGG
Found at i:1239940 original size:42 final size:42
Alignment explanation
Indices: 1239852--1239940 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
1239842 TAGCCCTCAA
*
1239852 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
* * * * *
1239894 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAAT
1 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
1239936 AGAGA
1 AGAGA
1239941 GAGGAGGGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.45, C:0.01, G:0.44, T:0.10
Consensus pattern (42 bp):
AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
Found at i:1250898 original size:12 final size:11
Alignment explanation
Indices: 1250876--1250993 Score: 54
Period size: 12 Copynumber: 10.9 Consensus size: 11
1250866 AGAGAAAGAA
*
1250876 GAGAGAGGAGG
1 GAGATAGGAGG
1250887 GATGATAGGAGG
1 GA-GATAGGAGG
*
1250899 AGAGACAGGA--
1 -GAGATAGGAGG
*
1250909 GAGATAGTA--
1 GAGATAGGAGG
1250918 GAGATAGGAGG
1 GAGATAGGAGG
1250929 GATGATAGGAGG
1 GA-GATAGGAGG
*
1250941 AGAGACAGGA--
1 -GAGATAGGAGG
**
1250951 GAGATA--ACA
1 GAGATAGGAGG
*
1250960 GAGAGAGGAGG
1 GAGATAGGAGG
1250971 GATGATAGGAGG
1 GA-GATAGGAGG
*
1250983 AGAGACAGGAG
1 -GAGATAGGAG
1250994 AGATAATAGA
Statistics
Matches: 83, Mismatches: 12, Indels: 23
0.70 0.10 0.19
Matches are distributed among these distances:
7 1 0.01
9 25 0.30
11 7 0.08
12 44 0.53
13 6 0.07
ACGTcount: A:0.41, C:0.03, G:0.47, T:0.08
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1250927 original size:42 final size:42
Alignment explanation
Indices: 1250875--1251026 Score: 268
Period size: 42 Copynumber: 3.6 Consensus size: 42
1250865 AAGAGAAAGA
*
1250875 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
* *
1250917 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAC
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1250959 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
1251001 AGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGAGAGGAGGGATGATAGGAGGAG
1251027 GAGAGAAGAA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 104 1.00
ACGTcount: A:0.41, C:0.03, G:0.47, T:0.09
Consensus pattern (42 bp):
AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:1250968 original size:18 final size:18
Alignment explanation
Indices: 1250941--1251032 Score: 60
Period size: 18 Copynumber: 4.8 Consensus size: 18
1250931 TGATAGGAGG
*
1250941 AGAGACAGGAGAGATAAC
1 AGAGAGAGGAGAGATAAC
*
1250959 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGAGAGGA--GA-GATA--A-C
* *
1250983 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAC
* *
1251001 AGAGAGAGGAGGGATGAC
1 AGAGAGAGGAGAGATAAC
1251019 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
1251033 AGAAGATGGA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
17 2 0.03
18 33 0.57
19 1 0.02
20 2 0.03
21 8 0.14
22 2 0.03
23 1 0.02
24 9 0.16
ACGTcount: A:0.43, C:0.04, G:0.46, T:0.07
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAC
Found at i:1257061 original size:42 final size:43
Alignment explanation
Indices: 1257011--1257269 Score: 162
Period size: 42 Copynumber: 6.2 Consensus size: 43
1257001 GCCAATAGGT
* *
1257011 AAAC-AAGGGAT-AAGAAGTCTCCTAGGTCAAAACTGATTGGC
1 AAACAAAGGGATAAAGAAGTCTCCTAGGTCAAAACCGATGGGC
* * * *
1257052 AGACAAAGGG-TAAAAAAATCTCCT-GAGTCAAAGCCGATGGGC
1 AAACAAAGGGATAAAGAAGTCTCCTAG-GTCAAAACCGATGGGC
* ** * * * **
1257094 AAACAAAGAGATGGAGAAGTCTCCCAGGTCTAAGCCGACAGGC
1 AAACAAAGGGATAAAGAAGTCTCCTAGGTCAAAACCGATGGGC
* ** * *
1257137 AAACGAAGGG-TAAAGAAGTCTTTTGGGTCAAAGCCGATGGGC
1 AAACAAAGGGATAAAGAAGTCTCCTAGGTCAAAACCGATGGGC
* * *
1257179 AAACTAAA--GATAAAG-AGTCT-CTCGGGTCTAAGCCGATGGGC
1 AAAC-AAAGGGATAAAGAAGTCTCCT-AGGTCAAAACCGATGGGC
* * *
1257220 AAACATAA--GATAAAGAAAGTCTCCCAAGTCTAAACCGATGGGC
1 AAACA-AAGGGATAAAG-AAGTCTCCTAGGTCAAAACCGATGGGC
*
1257263 AGACAAA
1 AAACAAA
1257270 TGGTTCGATG
Statistics
Matches: 171, Mismatches: 35, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
40 2 0.01
41 41 0.24
42 70 0.41
43 56 0.33
44 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (43 bp):
AAACAAAGGGATAAAGAAGTCTCCTAGGTCAAAACCGATGGGC
Found at i:1257129 original size:43 final size:42
Alignment explanation
Indices: 1257082--1257269 Score: 180
Period size: 43 Copynumber: 4.5 Consensus size: 42
1257072 TCCTGAGTCA
**
1257082 AAGCCGATGGGCAAACAAAGAGATGGAGAAGTCTCCCAGGTCT
1 AAGCCGATGGGCAAACAAA-AGATAAAGAAGTCTCCCAGGTCT
** * * * **** *
1257125 AAGCCGACAGGCAAACGAAGGGTAAAGAAGTCTTTTGGGTCA
1 AAGCCGATGGGCAAACAAAAGATAAAGAAGTCTCCCAGGTCT
* * *
1257167 AAGCCGATGGGCAAACTAAAGATAAAG-AGTCTCTCGGGTCT
1 AAGCCGATGGGCAAACAAAAGATAAAGAAGTCTCCCAGGTCT
* *
1257208 AAGCCGATGGGCAAACATAAGATAAAGAAAGTCTCCCAAGTCT
1 AAGCCGATGGGCAAACAAAAGATAAAG-AAGTCTCCCAGGTCT
* *
1257251 AAACCGATGGGCAGACAAA
1 AAGCCGATGGGCAAACAAA
1257270 TGGTTCGATG
Statistics
Matches: 115, Mismatches: 28, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
41 36 0.31
42 36 0.31
43 43 0.37
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (42 bp):
AAGCCGATGGGCAAACAAAAGATAAAGAAGTCTCCCAGGTCT
Found at i:1257146 original size:85 final size:83
Alignment explanation
Indices: 1257057--1257223 Score: 208
Period size: 85 Copynumber: 2.0 Consensus size: 83
1257047 TTGGCAGACA
**
1257057 AAGGGTAAAAAAATCTCCTGAGTCAAAGCCGATGGGCAAACAAAGAGATGGAGAAGTCTCCCAGG
1 AAGGGTAAAAAAATCTCCTGAGTCAAAGCCGATGGGCAAACAAA-AGATAAAG-AGTCTCCCAGG
1257122 TCTAAGCCGACAGGCAAACG
64 TCTAAGCCGACAGGCAAACG
* * ** * * * *
1257142 AAGGGTAAAGAAGTCTTTTGGGTCAAAGCCGATGGGCAAACTAAAGATAAAGAGTCTCTCGGGTC
1 AAGGGTAAAAAAATCTCCTGAGTCAAAGCCGATGGGCAAACAAAAGATAAAGAGTCTCCCAGGTC
**
1257207 TAAGCCGATGGGCAAAC
66 TAAGCCGACAGGCAAAC
1257224 ATAAGATAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
83 26 0.37
84 6 0.09
85 38 0.54
ACGTcount: A:0.37, C:0.19, G:0.28, T:0.16
Consensus pattern (83 bp):
AAGGGTAAAAAAATCTCCTGAGTCAAAGCCGATGGGCAAACAAAAGATAAAGAGTCTCCCAGGTC
TAAGCCGACAGGCAAACG
Found at i:1257234 original size:83 final size:86
Alignment explanation
Indices: 1257078--1257241 Score: 210
Period size: 83 Copynumber: 1.9 Consensus size: 86
1257068 AATCTCCTGA
**
1257078 GTCAAAGCCGATGGGCAAACAAAGAGATGGAGAAGTCTCCCAGGTCTAAGCCGACAGGCAAACGA
1 GTCAAAGCCGATGGGCAAACAAAGAGATAAAGAAGTCTCCCAGGTCTAAGCCGACAGGCAAACGA
* *
1257143 AGGGTAAAG-AAGTCTTTTGG
66 AAGATAAAGAAAGTCTTTTGG
* * * **
1257163 GTCAAAGCCGATGGGCAAACTAA-AGATAAAG-AGTCTCTCGGGTCTAAGCCGATGGGCAAAC-A
1 GTCAAAGCCGATGGGCAAACAAAGAGATAAAGAAGTCTCCCAGGTCTAAGCCGACAGGCAAACGA
1257225 TAAGATAAAGAAAGTCT
66 -AAGATAAAGAAAGTCT
1257242 CCCAAGTCTA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
82 1 0.01
83 33 0.49
84 12 0.18
85 22 0.32
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.16
Consensus pattern (86 bp):
GTCAAAGCCGATGGGCAAACAAAGAGATAAAGAAGTCTCCCAGGTCTAAGCCGACAGGCAAACGA
AAGATAAAGAAAGTCTTTTGG
Found at i:1257644 original size:84 final size:85
Alignment explanation
Indices: 1257586--1257785 Score: 278
Period size: 84 Copynumber: 2.4 Consensus size: 85
1257576 TTTATTGGGA
*
1257586 ACTAAACTGATAAGTAAACAATGGATGAAGGTTAACCGAAGACTGAGCTGACAGGTCACCATAAG
1 ACTAAACCGATAAGTAAACAATGGATGAAGGTTAACCGAAGACTGAGCTGACAGGTCACCATAAG
*
1257651 GGCAA-TAAGTTTACCGAAG
66 GGTAATTAAGTTTACCGAAG
* * *
1257670 ACTAAGCCGATAGGTAAACAATGGATGAAGGTTGACCGAAGACTGAGCTGACAGGTCACCATAAG
1 ACTAAACCGATAAGTAAACAATGGATGAAGGTTAACCGAAGACTGAGCTGACAGGTCACCATAAG
** *
1257735 GGTAA-TGGGTTTACCGAGG
66 GGTAATTAAGTTTACCGAAG
* * **
1257754 GCTAAGCCGACGAGTAAACAATGGATGAAGGT
1 ACTAAACCGATAAGTAAACAATGGATGAAGGT
1257786 AAACAATGAG
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 104 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (85 bp):
ACTAAACCGATAAGTAAACAATGGATGAAGGTTAACCGAAGACTGAGCTGACAGGTCACCATAAG
GGTAATTAAGTTTACCGAAG
Found at i:1257713 original size:41 final size:41
Alignment explanation
Indices: 1257594--1257713 Score: 109
Period size: 43 Copynumber: 2.9 Consensus size: 41
1257584 GAACTAAACT
* * *
1257594 GATAAGTAAACAATGGATGAAGGTTAACCGAAGACTGAGCT
1 GATAGGTAAACAATGGATGAAGGTTAACCGAAGACTAAGCC
* * * * *
1257635 GACAGGTCACCATAAGGGCAAT-AA-GTTTACCGAAGACTAAGCC
1 GATAGGT-A-AACAATGG--ATGAAGGTTAACCGAAGACTAAGCC
*
1257678 GATAGGTAAACAATGGATGAAGGTTGACCGAAGACT
1 GATAGGTAAACAATGGATGAAGGTTAACCGAAGACT
1257714 GAGCTGACAG
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 23 0.38
42 2 0.03
43 27 0.45
44 2 0.03
45 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (41 bp):
GATAGGTAAACAATGGATGAAGGTTAACCGAAGACTAAGCC
Found at i:1258001 original size:42 final size:42
Alignment explanation
Indices: 1257913--1258073 Score: 141
Period size: 42 Copynumber: 3.8 Consensus size: 42
1257903 GAGCCAACAG
* * *
1257913 GCAGAC-AAAGAATGAAAAAGTCTCTTGAGTCTAAGTTGAA-GA
1 GCAGACGAAAG-ATAAAAAAGTCTCTCGAGTCTAAG-TCAATGA
* * *
1257955 GCAGACAAAAGATAAAAAAGTCTCCTGGA-TCTAAGTCAATGG
1 GCAGACGAAAGATAAAAAAGTCT-CTCGAGTCTAAGTCAATGA
* *
1257997 GCAGACGAAAGA-AAAAGAAGTCTTTCGAGTCTAAGCCAATGA
1 GCAGACGAAAGATAAAA-AAGTCTCTCGAGTCTAAGTCAATGA
* ** * *
1258039 GCAGATGAAAGATAAATGAGTCTCCCAAGTCTAAG
1 GCAGACGAAAGATAAAAAAGTCTCTCGAGTCTAAG
1258074 CAAACGGGCA
Statistics
Matches: 98, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
41 10 0.10
42 77 0.79
43 11 0.11
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (42 bp):
GCAGACGAAAGATAAAAAAGTCTCTCGAGTCTAAGTCAATGA
Found at i:1258074 original size:42 final size:42
Alignment explanation
Indices: 1257953--1258093 Score: 110
Period size: 42 Copynumber: 3.4 Consensus size: 42
1257943 CTAAGTTGAA
* ** *
1257953 GAGCAGACAAAAGATAAAA-AAGTCT-CCTGGATCTAAGTCAAT
1 GAGCAGACGAAAGA-AAAAGAAGTCTCCCAAG-TCTAAGCCAAT
* ** *
1257995 GGGCAGACGAAAGAAAAAGAAGTCTTTCGAGTCTAAGCCAAT
1 GAGCAGACGAAAGAAAAAGAAGTCTCCCAAGTCTAAGCCAAT
* * * *
1258037 GAGCAGATGAAAGATAAATG-AGTCTCCCAAGTCTAAGCAAAC
1 GAGCAGACGAAAGA-AAAAGAAGTCTCCCAAGTCTAAGCCAAT
*
1258079 GGGCAGAC-AAAGAAA
1 GAGCAGACGAAAGAAA
1258094 GGATAAAGAA
Statistics
Matches: 80, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
40 2 0.03
41 9 0.11
42 63 0.79
43 6 0.08
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (42 bp):
GAGCAGACGAAAGAAAAAGAAGTCTCCCAAGTCTAAGCCAAT
Found at i:1258158 original size:43 final size:43
Alignment explanation
Indices: 1258091--1258189 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
1258081 GCAGACAAAG
* * *
1258091 AAAGGATAAAGAAGGTCTCCCGGGTCTAATCCGACT-GGTAGAC
1 AAAGGATAAAGAAGGTATCCCGGGTCTAAGCCGA-TGGGAAGAC
** * *
1258134 AAAGGATAAAGAAGGTATTTCGGGTTTGAGCCGATGGGAAGAC
1 AAAGGATAAAGAAGGTATCCCGGGTCTAAGCCGATGGGAAGAC
1258177 AAAGAGATAAAGA
1 AAAG-GATAAAGA
1258190 TTGCAATGAG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
42 1 0.02
43 38 0.81
44 8 0.17
ACGTcount: A:0.38, C:0.13, G:0.30, T:0.18
Consensus pattern (43 bp):
AAAGGATAAAGAAGGTATCCCGGGTCTAAGCCGATGGGAAGAC
Found at i:1258623 original size:78 final size:78
Alignment explanation
Indices: 1258522--1258975 Score: 484
Period size: 78 Copynumber: 5.8 Consensus size: 78
1258512 GTTCAAGAAA
* * * ** * *
1258522 AGGGATATGATTGGAAA-CATGTGGGAAGTGCCCCTCACGGCCATGTGATGCATCAATACCATTT
1 AGGGATATGACTGGAAATGA-GTAGGAAGTGCCCCTCTTGGCCATGTGATGCATCAATATCATCT
*
1258586 AGTATTTAAGAATG
65 AGTGTTTAAGAATG
* * * * * * * *
1258600 AGGGATATGATTAGAAAAGTGTGGGTAGTGCCCCTCTTGGCCATGTGATACATCAACATCATCTA
1 AGGGATATGACTGGAAATGAGTAGGAAGTGCCCCTCTTGGCCATGTGATGCATCAATATCATCTA
1258665 GTGTTTAAGAATG
66 GTGTTTAAGAATG
* * * *
1258678 AGGGATATGACTGGAAGTGAGTAGGAAATGCCCCTCTTGGCCATGTGATACATTAATATCATCTA
1 AGGGATATGACTGGAAATGAGTAGGAAGTGCCCCTCTTGGCCATGTGATGCATCAATATCATCTA
*
1258743 GTGTTTAGGAA-G
66 GTGTTTAAGAATG
* * *
1258755 AAGGGATATGACT-GAAAGCGAGTAGGAGGTGGCCCTCTTGGCCATGTGATGCATCAATATCATC
1 -AGGGATATGACTGGAAA-TGAGTAGGAAGTGCCCCTCTTGGCCATGTGATGCATCAATATCATC
*
1258819 TAGTGTTTGAGAATG
64 TAGTGTTTAAGAATG
* * * * * *
1258834 AGGGATACGACTGGAAGTGAGTGGGAAGTGCCCTTCTTGGCCATGTGATGCATCAATACCATTTA
1 AGGGATATGACTGGAAATGAGTAGGAAGTGCCCCTCTTGGCCATGTGATGCATCAATATCATCTA
* * *
1258899 GTATTTGAGAAAG
66 GTGTTTAAGAATG
* * * * * * *
1258912 AGGGATACGACTAG-AATGTGTAGGAAGTGCCCCTTTTCGCCTTGTGATGCATCAATATCCTCTA
1 AGGGATATGACTGGAAATGAGTAGGAAGTGCCCCTCTTGGCCATGTGATGCATCAATATCATCTA
1258976 AGGATTGGAT
Statistics
Matches: 318, Mismatches: 53, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
77 44 0.14
78 270 0.85
79 4 0.01
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (78 bp):
AGGGATATGACTGGAAATGAGTAGGAAGTGCCCCTCTTGGCCATGTGATGCATCAATATCATCTA
GTGTTTAAGAATG
Found at i:1259672 original size:88 final size:88
Alignment explanation
Indices: 1259579--1259745 Score: 253
Period size: 88 Copynumber: 1.9 Consensus size: 88
1259569 AAAATGATGG
* * * *
1259579 ATGCATGTGGAATGATGCAAATACTATTGTCATCTAAAATGCAGATACAGGTGAAACGATGCAAA
1 ATGCATATGGAATAATGCAAATACTAATGTCATCTAAAATGCAGATACAGGTGAAACGACGCAAA
*
1259644 TGTAAACATCAATAAAAAGGCAA
66 TGCAAACATCAATAAAAAGGCAA
* * *
1259667 ATGCATATGGAATAATGCAAATACTAATGTTATCTAAAATGTAGATGCAGGTGAAACGACGCAAA
1 ATGCATATGGAATAATGCAAATACTAATGTCATCTAAAATGCAGATACAGGTGAAACGACGCAAA
*
1259732 TGCAAGCATCAATA
66 TGCAAACATCAATA
1259746 GGAAGACAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 70 1.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (88 bp):
ATGCATATGGAATAATGCAAATACTAATGTCATCTAAAATGCAGATACAGGTGAAACGACGCAAA
TGCAAACATCAATAAAAAGGCAA
Found at i:1259761 original size:88 final size:88
Alignment explanation
Indices: 1259553--1259761 Score: 247
Period size: 88 Copynumber: 2.4 Consensus size: 88
1259543 GAAATGATGT
* * *** * * * *
1259553 AAATGCAAGCATCAATAAAATGATGGATGCATGTGGAATGATGCAAATACTATTGTCATCTAAAA
1 AAATGCAAACATCAATAAAAAGACAAAAGCATATGGAATAATGCAAATACTAATGTCATCTAAAA
*
1259618 TGCAGATACAGGTGAAACGATGC
66 TGCAGATACAGGTGAAACGACGC
* * * *
1259641 AAATGTAAACATCAATAAAAAGGCAAATGCATATGGAATAATGCAAATACTAATGTTATCTAAAA
1 AAATGCAAACATCAATAAAAAGACAAAAGCATATGGAATAATGCAAATACTAATGTCATCTAAAA
* *
1259706 TGTAGATGCAGGTGAAACGACGC
66 TGCAGATACAGGTGAAACGACGC
* **
1259729 AAATGCAAGCATCAATAGGAAGACAAAAGCATA
1 AAATGCAAACATCAATAAAAAGACAAAAGCATA
1259762 CAAAAAGATG
Statistics
Matches: 101, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
88 101 1.00
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (88 bp):
AAATGCAAACATCAATAAAAAGACAAAAGCATATGGAATAATGCAAATACTAATGTCATCTAAAA
TGCAGATACAGGTGAAACGACGC
Found at i:1259773 original size:88 final size:89
Alignment explanation
Indices: 1259592--1259784 Score: 237
Period size: 88 Copynumber: 2.2 Consensus size: 89
1259582 CATGTGGAAT
* * *
1259592 GATGCAAATACTATTGTCATCTAAAATGCAGATACAGGTGAAACGATGCAAATGTAAACATCAAT
1 GATGCAAATACTAATGTCATCTAAAATGCAGATACAGGTGAAACGACGCAAATGCAAACATCAAT
* * ** *
1259657 AAAAAGGCAAATGCATATGGAATA
66 AAAAAGACAAAAGCATATCAAAAA
* * * *
1259681 -ATGCAAATACTAATGTTATCTAAAATGTAGATGCAGGTGAAACGACGCAAATGCAAGCATCAAT
1 GATGCAAATACTAATGTCATCTAAAATGCAGATACAGGTGAAACGACGCAAATGCAAACATCAAT
**
1259745 AGGAAGACAAAAGCATA-CAAAAA
66 AAAAAGACAAAAGCATATCAAAAA
*
1259768 GATGCAAATACTGATGT
1 GATGCAAATACTAATGT
1259785 GGTCTAATTC
Statistics
Matches: 88, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
87 3 0.03
88 85 0.97
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (89 bp):
GATGCAAATACTAATGTCATCTAAAATGCAGATACAGGTGAAACGACGCAAATGCAAACATCAAT
AAAAAGACAAAAGCATATCAAAAA
Found at i:1263054 original size:8 final size:8
Alignment explanation
Indices: 1263038--1263073 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
1263028 AACGAAATAC
1263038 AAAAAAAT
1 AAAAAAAT
*
1263046 AATAAAAT
1 AAAAAAAT
*
1263054 AAAATAAT
1 AAAAAAAT
1263062 AAAAAAAT
1 AAAAAAAT
1263070 AAAA
1 AAAA
1263074 GATAGGGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1263057 original size:13 final size:13
Alignment explanation
Indices: 1263041--1263065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1263031 GAAATACAAA
1263041 AAAATAATAAAAT
1 AAAATAATAAAAT
1263054 AAAATAATAAAA
1 AAAATAATAAAA
1263066 AAATAAAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:1263509 original size:20 final size:20
Alignment explanation
Indices: 1263484--1263538 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1263474 TTTTACCTAG
* *
1263484 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTATGA
*
1263504 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTATGA
1263524 ATGTATCGATACATT
1 ATGTATCGATACATT
1263539 CTACTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTATGA
Found at i:1273559 original size:150 final size:152
Alignment explanation
Indices: 1273341--1273682 Score: 406
Period size: 150 Copynumber: 2.2 Consensus size: 152
1273331 ATAAAAATAA
* * * * * * * **
1273341 GATGAACCTATCCTACATGCTCACCTTTGGCACAAAAACAGACCTGGCGATAACTTAGGAATTAG
1 GATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGCAGACCCGGCGACAACCTAAAAATTAG
* * * *
1273406 TTTTGAAAAATTACTAAAATGCCCTTAGAGGAT-ACCTTTGACGTAGAAGTACATGATACCCCTA
66 TTTTGAAAAATTACTAAAATACCCTT--AGGATCACCTTTGACGTAAAAGTACATAACACCCCTA
*
1273470 AAGGACTTAAAAAG-GAT-AAA-G
129 AAGGACTTAAAAAGACATAAAAGG
*
1273491 GATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGC-GAACCCGGCGACAACCTAAAAATTG
1 GATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGCAG-ACCCGGCGACAACCTAAAAATTA
* * *
1273555 GTTTTGAAAAATTACTCAAATACCCTTAGGATCCACCTTTGACGTAAAAGTACCTAACACCCTTA
65 GTTTTGAAAAATTACTAAAATACCCTTAGGAT-CACCTTTGACGTAAAAGTACATAACACCCCTA
*
1273620 AGGGACTTAAAAAGATCATAAAAGG
129 AAGGACTTAAAAAGA-CATAAAAGG
** *
1273645 GATGAACCTATCCTAAATATCTACCTTTGGCATAAAAG
1 GATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAG
1273683 TGGACTCGGT
Statistics
Matches: 163, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
148 5 0.03
149 1 0.01
150 116 0.71
152 2 0.01
153 3 0.02
154 36 0.22
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (152 bp):
GATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGCAGACCCGGCGACAACCTAAAAATTAG
TTTTGAAAAATTACTAAAATACCCTTAGGATCACCTTTGACGTAAAAGTACATAACACCCCTAAA
GGACTTAAAAAGACATAAAAGG
Found at i:1273720 original size:154 final size:149
Alignment explanation
Indices: 1273406--1273791 Score: 418
Period size: 154 Copynumber: 2.6 Consensus size: 149
1273396 TAGGAATTAG
* * * *
1273406 TTTTGAAAAATTACTAAAATGCCCTTAGAGGATACCTTTGACGTAGAAGTACATGATACCCCTAA
1 TTTTGAAAAATTACTAAAATACCCTTA-AGGATACCTTTGACGTAAAAGTACCTGATACCCTTAA
* * *
1273471 AGGACTTAAAAAGGATAAAGGATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGCGAACCC
65 GGGACTTAAAAAGCATAAAGGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGAACCC
* *
1273536 GGCGACAACCTAAAAATTGG
130 GGCGACAACCTAAAAAGTGA
* * *
1273556 TTTTGAAAAATTACTCAAATACCCTT-AGGATCCACCTTTGACGTAAAAGTACCTAACACCCTTA
1 TTTTGAAAAATTACTAAAATACCCTTAAGGAT--ACCTTTGACGTAAAAGTACCTGATACCCTTA
* * *
1273620 AGGGACTTAAAAAGATCATAAAAGGGATGAACCTATCCTAAATATCTACCTTTGGCATAAAAGTG
64 AGGGACTTAAAAAG--CAT-AAA-GGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCG
* * * ** ** *
1273685 GACTCGGTGATGACCTAGGAGGTGA
125 AACCCGGCGACAACCTAAAAAGTGA
* * * *
1273710 TTTT-AGAAAATTACAAAAATACCTTTAAGGGATACCTTTGACATAAAAGTACCCGATACCCTTA
1 TTTTGA-AAAATTACTAAAATACCCTTAA-GGATACCTTTGACGTAAAAGTACCTGATACCCTTA
*
1273774 AGGGATTTAAAAA-CATAA
64 AGGGACTTAAAAAGCATAA
1273792 GGGAATGTAT
Statistics
Matches: 196, Mismatches: 31, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
148 5 0.03
150 65 0.33
151 3 0.02
152 2 0.01
153 4 0.02
154 112 0.57
155 1 0.01
156 4 0.02
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (149 bp):
TTTTGAAAAATTACTAAAATACCCTTAAGGATACCTTTGACGTAAAAGTACCTGATACCCTTAAG
GGACTTAAAAAGCATAAAGGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGAACCCG
GCGACAACCTAAAAAGTGA
Found at i:1275533 original size:12 final size:12
Alignment explanation
Indices: 1275516--1275563 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1275506 TCCTTCTCCA
*
1275516 TTTTTTATTCCT
1 TTTTTTATTTCT
*
1275528 TTTTTTTTTTCT
1 TTTTTTATTTCT
*
1275540 TTTTTGATTTCT
1 TTTTTTATTTCT
1275552 TTCTTTTCATTT
1 TT-TTTT-ATTT
1275564 AATTTTGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 22 0.76
13 3 0.10
14 4 0.14
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTTTATTTCT
Found at i:1276110 original size:167 final size:167
Alignment explanation
Indices: 1275879--1276412 Score: 667
Period size: 169 Copynumber: 3.2 Consensus size: 167
1275869 AAAAAATAAG
* * * ** * *
1275879 AAATAAATTGAATTTTACAAAACTGATTAAATGGGAATTAAATAACAATATTAGATAAATTTTAA
1 AAATGAATTAAATTTT-CAAAACTGATTTAATGGGAATTCCATAATATTATTAGATAAATTTTAA
* * * * * * * *
1275944 AATTTTTAAATC-AAGAAAAATCCCCCTCAAAATATTTACGGAGTAGAAAACTCGATTTTTTAGG
65 AAATTTTAGACCAAAG-AAAATCCTCCTAAAAATATTTATGGAATAGAAAACTCGATTTTTTGGG
* * * * **
1276008 AAAATAGTCAATTCAAGGAAAAAAATAAAAAACTCATGA
129 AAAAAAGTGATTTCAAAGAAAAAAATCCAAAACTCATGA
* * * *
1276047 AAATGAATTAAATTTTCAAAACTAATTTAATGGGAATTCCATGATATTATTAAATACATTTTAAA
1 AAATGAATTAAATTTTCAAAACTGATTTAATGGGAATTCCATAATATTATTAGATAAATTTTAAA
* *
1276112 AATTTTAGACCAAAGAAAATTCTCCTAAAAATATTTATGGAATAGGAAACTCGATTTTTTGGGAA
66 AATTTTAGACCAAAGAAAATCCTCCTAAAAATATTTATGGAATAGAAAACTCGATTTTTTGGG-A
*
1276177 AAAAAATGATTTCAAAGAAGAAAAATCCAAAACTCATGA
130 AAAAAGTGATTTCAAAGAA-AAAAATCCAAAACTCATGA
* * * *
1276216 ATATGAGTTAAATTTTTAAAACCGATTTAATGGGAATTCCATAATATTATTAGATAAATTTTAAA
1 AAATGAATTAAATTTTCAAAACTGATTTAATGGGAATTCCATAATATTATTAGATAAATTTTAAA
* * * *
1276281 AATTTTAGACCAAAGAAAATCCTCCTGAAAATATTTATTGAATAGAAAACTTGATTTTTCGGGAA
66 AATTTTAGACCAAAGAAAATCCTCCTAAAAATATTTATGGAATAGAAAACTCGATTTTTTGGGAA
** *
1276346 AAGGGAGATTTCAAAG-AAAAAATCCAAAACTCATGA
131 AAAAGTGATTTCAAAGAAAAAAATCCAAAACTCATGA
1276382 AAATGAATTAAATTTTCAAAACTGATTTAAT
1 AAATGAATTAAATTTTCAAAACTGATTTAAT
1276413 ATGATTTAAA
Statistics
Matches: 313, Mismatches: 50, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
166 46 0.15
167 90 0.29
168 46 0.15
169 131 0.42
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.31
Consensus pattern (167 bp):
AAATGAATTAAATTTTCAAAACTGATTTAATGGGAATTCCATAATATTATTAGATAAATTTTAAA
AATTTTAGACCAAAGAAAATCCTCCTAAAAATATTTATGGAATAGAAAACTCGATTTTTTGGGAA
AAAAGTGATTTCAAAGAAAAAAATCCAAAACTCATGA
Found at i:1278025 original size:81 final size:80
Alignment explanation
Indices: 1277884--1278044 Score: 304
Period size: 81 Copynumber: 2.0 Consensus size: 80
1277874 GTCCAAAGTA
*
1277884 AGTCACAACCAATAGGGCCCTTTATTACAAATGATTAAATTAACTCAAGTCCTAATTCAATCCAT
1 AGTCACAACCAACAGGGCCCTTTATTACAAATGATTAAATTAACTCAAGTCCTAATTCAATCCAT
1277949 TGGAGCCCATATCTT
66 TGGAGCCCATATCTT
1277964 AGTCACAACCAACAGGGCCCTTTATTACAAAGTGATTAAATTAACTCAAGTCCTAATTCAATCCA
1 AGTCACAACCAACAGGGCCCTTTATTACAAA-TGATTAAATTAACTCAAGTCCTAATTCAATCCA
1278029 TTGGAGCCCATATCTT
65 TTGGAGCCCATATCTT
1278045 CTGAATATAT
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
80 30 0.38
81 49 0.62
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (80 bp):
AGTCACAACCAACAGGGCCCTTTATTACAAATGATTAAATTAACTCAAGTCCTAATTCAATCCAT
TGGAGCCCATATCTT
Found at i:1278411 original size:26 final size:27
Alignment explanation
Indices: 1278382--1278435 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
1278372 CTATAATCGA
*
1278382 TAGTGGAATCAGGA-AATTCCAATCCC
1 TAGTGGAACCAGGAGAATTCCAATCCC
*
1278408 TAGTGGAACCAGGATGAATTGCAATCCC
1 TAGTGGAACCAGGA-GAATTCCAATCCC
1278436 CATTAAAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 13 0.54
28 11 0.46
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTGGAACCAGGAGAATTCCAATCCC
Found at i:1279238 original size:34 final size:34
Alignment explanation
Indices: 1279160--1279424 Score: 220
Period size: 34 Copynumber: 7.7 Consensus size: 34
1279150 AAATCTTCTT
* *
1279160 AAGTCCACGCAAGTCGATGGCAACCAAACCTTTTCCA
1 AAGTCCACACAAGTCGGTGGC-A-CAAACCTTTT-CA
*
1279197 AAGTCCACACAAGTTGGTGGCACAAA-CTTTCTCA
1 AAGTCCACACAAGTCGGTGGCACAAACCTTT-TCA
1279231 AAGTCCACACAAGTCGGTGGCAACTAAACCTTTTCCA
1 AAGTCCACACAAGTCGGTGGC-AC-AAACCTTTT-CA
* * * * *
1279268 AAGTCTACATAA--C-CTGGCAGC-ATCCTTTCCA
1 AAGTCCACACAAGTCGGTGGCA-CAAACCTTTTCA
* * * * *
1279299 AAGTCTACATAACTCGATGGCACAAACCTTTTTA
1 AAGTCCACACAAGTCGGTGGCACAAACCTTTTCA
* * *
1279333 AAGTCCACATAAGTCGATGGCAAAAACCTTTTCA
1 AAGTCCACACAAGTCGGTGGCACAAACCTTTTCA
*
1279367 AAGTCCACACAAGTCGGTGGCAACCAAACCCTTTTAA
1 AAGTCCACACAAGTCGGTGGC-A-CAAA-CCTTTTCA
*
1279404 AAG-CC-CATAAGTCGGTGGCAC
1 AAGTCCACACAAGTCGGTGGCAC
1279425 CCAAAGCCCA
Statistics
Matches: 193, Mismatches: 22, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
31 14 0.07
32 6 0.03
33 4 0.02
34 93 0.48
35 22 0.11
36 10 0.05
37 44 0.23
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (34 bp):
AAGTCCACACAAGTCGGTGGCACAAACCTTTTCA
Found at i:1279492 original size:30 final size:29
Alignment explanation
Indices: 1279399--1279495 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 29
1279389 ACCAAACCCT
* *
1279399 TTTAAAAGCCCATAAGTCGGTGGCACC-C
1 TTTAAAAGCCCACAAGTCAGTGGCACCAC
* *
1279427 ----AAAGCCCATAAGTCAGTGGCACCCC
1 TTTAAAAGCCCACAAGTCAGTGGCACCAC
* *
1279452 TTTCAAAGCCCACAAGTCAGTGGCACCAT
1 TTTAAAAGCCCACAAGTCAGTGGCACCAC
1279481 TTTAAAAAGCCCACA
1 TTT-AAAAGCCCACA
1279496 CAAGCTGGTG
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
24 22 0.38
25 1 0.02
29 25 0.43
30 10 0.17
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.19
Consensus pattern (29 bp):
TTTAAAAGCCCACAAGTCAGTGGCACCAC
Found at i:1279922 original size:18 final size:21
Alignment explanation
Indices: 1279877--1279930 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 21
1279867 TATAACAAAT
*
1279877 CAATGTATCGATACATAAGTG
1 CAATGTATCGATACATAAGTA
1279898 C-ATGTATCGATAC-T-AG-A
1 CAATGTATCGATACATAAGTA
*
1279915 CAATGTATCAATACAT
1 CAATGTATCGATACAT
1279931 TACTCATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 1 0.03
18 13 0.45
19 2 0.07
20 12 0.41
21 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (21 bp):
CAATGTATCGATACATAAGTA
Found at i:1281143 original size:28 final size:28
Alignment explanation
Indices: 1281090--1281143 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
1281080 CTTGATTCCT
*
1281090 TTTCCTTTGCAATTTCTTGCTTATTTTG
1 TTTCCTTTGCAATTTCTTGATTATTTTG
1281118 TTTCCTTT-CATATTTCTT-ATTGATTT
1 TTTCCTTTGCA-ATTTCTTGATT-ATTT
1281144 CACTTCCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (28 bp):
TTTCCTTTGCAATTTCTTGATTATTTTG
Found at i:1289446 original size:12 final size:12
Alignment explanation
Indices: 1289429--1289453 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1289419 TATTTTTGGA
1289429 ATATTAAGTCGG
1 ATATTAAGTCGG
1289441 ATATTAAGTCGG
1 ATATTAAGTCGG
1289453 A
1 A
1289454 CCCCTAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (12 bp):
ATATTAAGTCGG
Found at i:1295875 original size:42 final size:42
Alignment explanation
Indices: 1295820--1295938 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1295810 TTCTTCTCTC
* *
1295820 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1295862 CTCCTCCTATCATCCCTCCTATCTTTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1295904 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1295939 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1295880 original size:24 final size:24
Alignment explanation
Indices: 1295844--1295929 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1295834 CCTCCTCTCT
* *
1295844 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1295868 CTATCATCCCTCCTATCT-T--TA
1 CTATCATCCCTCCTGTCTCTCCTC
1295889 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1295910 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1295930 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 8 0.16
19 1 0.02
20 1 0.02
21 12 0.24
22 1 0.02
23 1 0.02
24 25 0.51
ACGTcount: A:0.10, C:0.44, G:0.02, T:0.43
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1303789 original size:18 final size:19
Alignment explanation
Indices: 1303747--1303796 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
1303737 TCCATCTTCT
1303747 TCTCTCCTC-CTCTTGTCA
1 TCTCTCCTCTCTCTTGTCA
*
1303765 TCCCTCCTCTCTCTAT-T-A
1 TCTCTCCTCTCTCT-TGTCA
*
1303783 TCTCTCCTGTCTCT
1 TCTCTCCTCTCTCT
1303797 CCTCCTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 21 0.78
19 5 0.19
20 1 0.04
ACGTcount: A:0.06, C:0.44, G:0.04, T:0.46
Consensus pattern (19 bp):
TCTCTCCTCTCTCTTGTCA
Found at i:1303808 original size:42 final size:42
Alignment explanation
Indices: 1303753--1303871 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1303743 TTCTTCTCTC
* * *
1303753 CTCCTCTTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
1303795 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1303837 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1303872 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1303812 original size:12 final size:11
Alignment explanation
Indices: 1303786--1303861 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1303776 TCTATTATCT
*
1303786 CTCCTGTCTCTC
1 CTCCTATCTC-C
1303798 CTCCTATCATCC
1 CTCCTATC-TCC
1303810 CTCCTATCT--
1 CTCCTATCTCC
*
1303819 CTACTATCT--
1 CTCCTATCTCC
*
1303828 CTCCTGTCTCTC
1 CTCCTATCTC-C
1303840 CTCCTATCATCC
1 CTCCTATC-TCC
*
1303852 CTCCTCTCTC
1 CTCCTATCTC
1303862 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:1303813 original size:24 final size:24
Alignment explanation
Indices: 1303777--1303862 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1303767 CCTCCTCTCT
* *
1303777 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1303801 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1303822 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1303843 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1303863 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1303837 original size:18 final size:18
Alignment explanation
Indices: 1303768--1303838 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1303758 CTTGTCATCC
* *
1303768 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
1303786 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
1303808 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
1303828 CTCCTGTCTCT
1 CTCCTGTCTCT
1303839 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:1314801 original size:19 final size:18
Alignment explanation
Indices: 1314738--1314806 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 18
1314728 GTTGGGCTTA
*
1314738 ATGTATTGATACATTCAT
1 ATGTATCGATACATTCAT
1314756 CATGTATCGATACAATTCAAAT
1 -ATGTATCGATAC-ATTC--AT
*
1314778 ATGTATCGATACATGCACT
1 ATGTATCGATACATTCA-T
1314797 ATGTATCGAT
1 ATGTATCGAT
1314807 CCAATTGTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.02
19 22 0.50
20 7 0.16
21 12 0.27
22 2 0.05
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (18 bp):
ATGTATCGATACATTCAT
Found at i:1314894 original size:13 final size:13
Alignment explanation
Indices: 1314876--1314900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1314866 TACAAAGAAC
1314876 ATGTATCGATACA
1 ATGTATCGATACA
1314889 ATGTATCGATAC
1 ATGTATCGATAC
1314901 CAAGTAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1315983 original size:21 final size:21
Alignment explanation
Indices: 1315942--1315983 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1315932 GACTTGAGCT
*
1315942 GCTGACTCATCATATCTAAGC
1 GCTGACTCATCATATCAAAGC
*
1315963 GCTGA-TCTATCATGTCAAAGC
1 GCTGACTC-ATCATATCAAAGC
1315984 ATTGATCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (21 bp):
GCTGACTCATCATATCAAAGC
Found at i:1322489 original size:42 final size:42
Alignment explanation
Indices: 1322434--1322552 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1322424 TTCTTCTCTC
* *
1322434 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
1322476 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1322518 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1322553 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1322493 original size:12 final size:11
Alignment explanation
Indices: 1322467--1322542 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1322457 TCTATTATCT
*
1322467 CTCCTGTCTCTC
1 CTCCTATCTC-C
1322479 CTCCTATCATCC
1 CTCCTATC-TCC
1322491 CTCCTATCT--
1 CTCCTATCTCC
*
1322500 CTACTATCT--
1 CTCCTATCTCC
*
1322509 CTCCTGTCTCTC
1 CTCCTATCTC-C
1322521 CTCCTATCATCC
1 CTCCTATC-TCC
*
1322533 CTCCTCTCTC
1 CTCCTATCTC
1322543 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:1322494 original size:24 final size:24
Alignment explanation
Indices: 1322458--1322543 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1322448 CCTCCTCTCT
* *
1322458 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1322482 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1322503 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1322524 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1322544 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1322518 original size:18 final size:18
Alignment explanation
Indices: 1322449--1322519 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1322439 CCTGTCATCC
* *
1322449 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
1322467 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
1322489 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
1322509 CTCCTGTCTCT
1 CTCCTGTCTCT
1322520 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:1324522 original size:12 final size:11
Alignment explanation
Indices: 1324500--1324566 Score: 66
Period size: 12 Copynumber: 5.9 Consensus size: 11
1324490 AGAGAAAGAA
*
1324500 GAGATAAGAGG
1 GAGATAGGAGG
1324511 GATGATAGGAGG
1 GA-GATAGGAGG
*
1324523 AGAGATAGTA--
1 -GAGATAGGAGG
1324533 GAGATAGGAGG
1 GAGATAGGAGG
1324544 GATGATAGGAGG
1 GA-GATAGGAGG
1324556 AGAGATAGGAG
1 -GAGATAGGAG
1324567 AGATAATAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
9 8 0.17
11 4 0.09
12 31 0.66
13 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.46, T:0.13
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1324527 original size:33 final size:33
Alignment explanation
Indices: 1324490--1324572 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
1324480 TAGCCATCAA
*
1324490 AGAGAAAGAAGAGATAAGAGGGATGATAGGAGG
1 AGAGATAGAAGAGATAAGAGGGATGATAGGAGG
* *
1324523 AGAGATAGTAGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGAAGAGATAAGAGGGATGATAGGAGG
*
1324556 AGAGATAGGAGAGATAA
1 AGAGATAGAAGAGATAA
1324573 TAGAGAGAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.00, G:0.42, T:0.12
Consensus pattern (33 bp):
AGAGATAGAAGAGATAAGAGGGATGATAGGAGG
Found at i:1324575 original size:12 final size:12
Alignment explanation
Indices: 1324511--1324582 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
1324501 AGATAAGAGG
1324511 GATGATAGGAGGA
1 GATGATAGGA-GA
*
1324524 GA-GATA-G-TA
1 GATGATAGGAGA
*
1324533 GA-GATAGGAGG
1 GATGATAGGAGA
1324544 GATGATAGGAGGA
1 GATGATAGGA-GA
1324557 GA-GATAGGAGA
1 GATGATAGGAGA
*
1324568 GATAATAGAGAGA
1 GATGATAG-GAGA
1324581 GA
1 GA
1324583 AGGGATGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
9 7 0.15
10 1 0.02
11 7 0.15
12 22 0.46
13 11 0.23
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (12 bp):
GATGATAGGAGA
Found at i:1327691 original size:18 final size:18
Alignment explanation
Indices: 1327668--1327712 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1327658 AAAGGGGTTT
1327668 CATGATGGGTTTTTCAAG
1 CATGATGGGTTTTTCAAG
*
1327686 CATGATGGGTTTTTCAAT
1 CATGATGGGTTTTTCAAG
*
1327704 TATGATGGG
1 CATGATGGG
1327713 AATTTGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.09, G:0.29, T:0.40
Consensus pattern (18 bp):
CATGATGGGTTTTTCAAG
Found at i:1332934 original size:12 final size:11
Alignment explanation
Indices: 1332912--1332987 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1332902 AGAGAAAGAA
*
1332912 GAGAGAGGAGG
1 GAGATAGGAGG
1332923 GATGATAGGAGG
1 GA-GATAGGAGG
*
1332935 AGAGACAGGA--
1 -GAGATAGGAGG
*
1332945 GAGATAGTA--
1 GAGATAGGAGG
1332954 GAGATAGGAGG
1 GAGATAGGAGG
1332965 GATGATAGGAGG
1 GA-GATAGGAGG
*
1332977 AGAGACAGGAG
1 -GAGATAGGAG
1332988 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Done.